Integrative bioinformatics analysis identifies LINC01614 as a potential prognostic signature in esophageal cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35116503", "kind": "science-record", "revision": 5, "content_hash": "sha256:7616b2d2247183f17fbbf587fbf05aef08f982d37a6782db33c42c911b2aab0a", "created_at": "2026-11-01T17:36:50Z", "updated_at": "2026-11-01T22:48:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrative bioinformatics analysis identifies LINC01614 as a potential prognostic signature in esophageal cancer.", "doi": "10.21037/tcr-20-2529", "pmid": "35116503", "authors": ["Shuo Yan", "Jichong Xu", "Bingyan Liu", "Lin Ma", "Huaqiao Tan", "Chun Fang"], "journal": "Translational cancer research", "year": 2021, "abstract": "BACKGROUND: Esophageal cancer (EC) is one of the most common gastrointestinal cancers and the incidence is on the increase in recent years. The aim of the present study was to assess novel long non-coding RNA (lncRNA) biomarkers for the prognosis of EC through the analysis of gene expression microarrays.\nMETHODS: Three datasets (GSE53622, GSE53624, and GSE53625) were downloaded from the Gene Expression Omnibus (GEO) database and EC patients' clinical information were from The Cancer Genome Atlas (TCGA) databases. Differentially expressed genes (DEGs) were screened by comparing tumor tissues with normal tissues using limma R package. The Gene Expression Profiling Interactive Analysis 2 (GEPIA2) database was used to obtain the novel lncRNAs and their co-expression genes in EC and these were visualized with the Cytoscape software. The Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology Based Annotation System (KOBAS) database was used to analyze the functions enrichment of selected DEGs. Cell Counting Kit-8 (CCK8) and Transwell assays were used to further confirm the function of target lncRNAs.\nRESULTS: We identified 24 differentially expressed (DE) lncRNAs and 659 DE mRNAs from the intersection of GEO and TCGA databases. And we found that only LINC01614 was concerned with a candidate prognostic signature in EC. \"Extracellular matrix (ECM)-receptor interaction\" and \"PI3K-Akt signaling pathway\" were observed, and we constructed a lncRNA-mRNA co-expression network for EC that includes LINC01614 and 64 mRNAs. The results of CCK8 and Transwell assays showed that suppression of LINC01614 inhibited EC cell proliferation and migration.\nCONCLUSIONS: Our study might provide LINC01614 as a novel lncRNA biomarker for diagnosis and prognosis in EC.", "claims": [{"id": "claim-method", "statement": "We performed differentially expressed (DE) mRNAs and lncRNAs with thresholds of |log fold change| >1 and adjusted P value <0.05 by comparing tumor tissues with normal tissues using limma R package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35116503", "locator": "sections[3] \"Public data collection and bioinformation analyses\" paragraph 2", "quote": "We performed differentially expressed (DE) mRNAs and lncRNAs with thresholds of |log fold change| >1 and adjusted P value <0.05 by comparing tumor tissues with normal tissues using limma R package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The details of three datasets (GSE53622, GSE53624, and GSE53625) were downloaded from GEO database, and EC RNA expression profiles were downloaded from TCGA database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35116503", "locator": "sections[3] \"Public data collection and bioinformation analyses\" paragraph 2", "quote": "The details of three datasets (GSE53622, GSE53624, and GSE53625) were downloaded from GEO database, and EC RNA expression profiles were downloaded from TCGA database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified LINC01614 as the only differentially expressed lncRNA associated with a candidate prognostic signature in esophageal cancer and showed that its suppression inhibited EC cell proliferation and migration.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35116503", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified 24 differentially expressed (DE) lncRNAs and 659 DE mRNAs from the intersection of GEO and TCGA databases. And we found that only LINC01614 was concerned with a candidate prognostic signature in EC. “Extracellular matrix (ECM)-receptor interaction” and “PI3K-Akt signaling pathway” were observed, and we constructed a lncRNA-mRNA co-expression network for EC that includes LINC01614 and 64 mRNAs. The results of CCK8 and Transwell assays showed that suppression of LINC01614 inhibited EC cell proliferation and migration."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified LINC01614 as the only differentially expressed lncRNA associated with a candidate prognostic signature in esophageal cancer and showed that its suppression inhibited EC cell proliferation and migration.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:35116503"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE53622"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE53622"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35116503", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-20-2529", "sha256": 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Cell Counting Kit-8 (CCK8) and Transwell assays were used to further c", "ludes LINC01614 and 64 mRNAs. The results of CCK8 and Transwell assays showed that suppression"], "order_basis": "paper_text_order:1096", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Methods Cell culture and siRNA transfection Human EC cell lines (EC9706, TE-1, and EC109", "ckdown experiments. 50 nM target siRNAs were transfected into EC109 and TE-1 cells using Lipofectamin", ") were synthesized by GenePharma and used in knockdown experiments. 50 nM target siRNAs were transf", "Methods Cell culture and siRNA transfection Human EC cell lines (EC9706, TE"], "order_basis": "paper_text_order:1884", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["y of Cell Resource Center (Shanghai, China). Cell lines were cultured in RPMI-1640 (Corning) supplemented with 10%", "ce Center (Shanghai, China). Cell lines were cultured in RPMI-1640 (Corning) supplemented with 10% Fe"], "order_basis": "paper_text_order:2064", "id": "assay:3"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We performed differentially expressed (DE) mRNAs and lncRNAs with thresholds of |log fold change| >1 and adjusted P value <0.05 by comparing tumor tissues with normal tissues using limma R package."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}